From 4831e7f2dece110dee88b3fe802d50b845ed9603 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 12 Oct 2006 16:14:02 +0000
Subject: [PATCH] Add features from Popupmenu

---
 src/jalview/gui/FeatureRenderer.java |   88 +++++++++++++++++++++++++++++++---
 src/jalview/gui/Finder.java          |   31 +++++-------
 src/jalview/gui/PopupMenu.java       |   45 +++++++++++++++++
 3 files changed, 139 insertions(+), 25 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index afe29a0..d20fa63 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -25,6 +25,10 @@ import java.awt.*;
 import java.util.*;
 
 import java.awt.image.*;
+import javax.swing.JComboBox;
+import javax.swing.JPanel;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
 
 
 /**
@@ -413,17 +417,87 @@ public class FeatureRenderer
     }
 
 
-    public void addNewFeature(String name, Color col, String group)
+    static String lastFeatureAdded = "feature_1";
+    static String lastSourceAdded = "Jalview";
+
+    public boolean createNewFeatures(SequenceI[] sequences,
+                                  SequenceFeature [] features)
     {
 
-      setColour(name, col);
-      if(av.featuresDisplayed==null)
-        av.featuresDisplayed = new Hashtable();
+      JComboBox name = new JComboBox();
+      JComboBox source = new JComboBox();
+
+      JPanel panel = new JPanel(new GridLayout(2, 2));
+      panel.add(new JLabel("New Sequence Feature Name"));
+      panel.add(name);
+      panel.add(new JLabel("Source:"));
+      panel.add(source);
+     // name.setPreferredSize(new Dimension(300, 20));
+      name.setEditable(true);
+      source.setEditable(true);
+
+      Enumeration en;
+      if (av.featuresDisplayed != null)
+      {
+        en = av.featuresDisplayed.keys();
+        while (en.hasMoreElements())
+        {
+          name.addItem(en.nextElement().toString());
+        }
+      }
+
+      if (featureGroups != null)
+      {
+        en = featureGroups.keys();
+        while (en.hasMoreElements())
+        {
+          source.addItem(en.nextElement().toString());
+        }
+      }
+
+      name.setSelectedItem(lastFeatureAdded);
+      source.setSelectedItem(lastSourceAdded);
 
-      if(group == null)
-        group = "NOGROUP";
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          panel, "Create New Sequence Feature(s)",
+          JOptionPane.OK_CANCEL_OPTION);
+
+
+      if(reply==JOptionPane.OK_OPTION
+         && name.getSelectedItem()!=null
+         && source.getSelectedItem()!=null)
+      {
+        lastFeatureAdded = name.getSelectedItem().toString();
+        lastSourceAdded = source.getSelectedItem().toString();
+        for(int i=0; i<sequences.length; i++)
+        {
+          features[i].type = lastFeatureAdded;
+          features[i].featureGroup = lastSourceAdded;
+          sequences[i].addSequenceFeature(features[i]);
+        }
+
+        if (av.featuresDisplayed == null)
+          av.featuresDisplayed = new Hashtable();
+
+        if(featureGroups==null)
+          featureGroups = new Hashtable();
+
+        featureGroups.put(lastSourceAdded, new Boolean(true));
+
+        Color col = getColour(lastFeatureAdded);
+        if(col==null)
+        {
+          col = new Color(60, 160, 115);
+          setColour(lastFeatureAdded, col);
+        }
+
+        av.featuresDisplayed.put(lastSourceAdded, new Integer(col.getRGB()));
+        findAllFeatures();
+        return true;
+      }
+      else
+        return false;
 
-      av.featuresDisplayed.put(name, new Integer(col.getRGB()));
     }
 
     public void setColour(String featureType, Color col)
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e8c16d2..8697552 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -114,34 +114,29 @@ public class Finder extends GFinder
         panel.add(label, BorderLayout.NORTH);
         panel.add(textinput, BorderLayout.SOUTH);
 
-         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            panel, "New Sequence Feature Name",
-          JOptionPane.OK_CANCEL_OPTION );
 
-         if(reply != JOptionPane.OK_OPTION)
-           return;
+        SequenceI [] seqs = new SequenceI[searchResults.getSize()];
+        SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];
+
 
         for (int i = 0; i < searchResults.getSize(); i ++ )
         {
-            SequenceI seq = searchResults.getResultSequence(i);
+            seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
 
-            SequenceFeature sf = new SequenceFeature(textinput.getText(),
+            features[i] = new SequenceFeature(textinput.getText(),
                 "Search Results", null,
                 searchResults.getResultStart(i),
-               searchResults.getResultEnd(i),
+                searchResults.getResultEnd(i),
                "Search Results");
-
-            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
-                textinput.getText(), new Color(60,160,115),
-                    "Search Results");
-
-            seq.getDatasetSequence().addSequenceFeature(sf);
         }
 
-        ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
-        ap.alignFrame.showSeqFeatures.setSelected(true);
-        av.setShowSequenceFeatures(true);
-        ap.highlightSearchResults(null);
+        if( ap.seqPanel.seqCanvas.getFeatureRenderer()
+            .createNewFeatures(seqs, features))
+        {
+          ap.alignFrame.showSeqFeatures.setSelected(true);
+          av.setShowSequenceFeatures(true);
+          ap.highlightSearchResults(null);
+        }
     }
 
     /**
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 88ea11b..c673af1 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -82,6 +82,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -504,12 +505,22 @@ public class PopupMenu extends JPopupMenu
       }
     });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
     groupMenu.addSeparator();
+    groupMenu.add(sequenceFeature);
+    groupMenu.addSeparator();
     groupMenu.add(groupName);
     groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
@@ -842,6 +853,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -1309,4 +1321,37 @@ public class PopupMenu extends JPopupMenu
     new jalview.io.DBRefFetcher(
              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
+
+  public void sequenceFeature_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize(false);
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+
+      features[i] = new SequenceFeature(
+          "",
+          "Search Results", null,
+          start,
+          end,
+          "Search Results");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
 }
-- 
1.7.10.2